User: umermehar10

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Posts by umermehar10

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Comment: C: Replacing the Chr names and position notions in vcf
... Dear I am trying with the script you have generously created for me, But I am receiving the following error IndentationError: unexpected indent >>> Chr1 = line.rstrip().split("\t")[1] although I am trying to maintain the correct indentation in command for line in match_f: ...
written 4 months ago by umermehar100
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Comment: C: Replacing the Chr names and position notions in vcf
... Thanks Bastien for this help ...
written 4 months ago by umermehar100
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Comment: C: Replacing the Chr names and position notions in vcf
... Thank you Dear For this guidance ...
written 4 months ago by umermehar100
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Comment: C: Replacing the Chr names and position notions in vcf
... Thank you Sir for this advice I will try to do it ...
written 4 months ago by umermehar100
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Replacing the Chr names and position notions in vcf
... Dear All I have a combined VCF file of few individuals. In this VCF instead of having normal CHR1, chr2 notions for chromosomes it is having the chromosome information as gi|996703411|ref|NW_015379183.1|, gi|996703411|ref|NW_015379175.1 In this notion `NW_015379183.1` corresponds to a specifi ...
vcf chromosome name replacement written 4 months ago by umermehar100 • updated 4 months ago by Bastien Hervé1.3k
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Variant calling in galaxy
... I am using galaxy GATKtools for variant callin. At unified genotyper SNP and INDEL caller I am unable to run the advance level of analysis as the options for annotation (Fisher Stand, Haplotype Score Homopolymerrun etc are not available in the list) they were available previously now I am unable to ...
next-gen snp written 9 months ago by umermehar100
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Comment: C: R for Amova Analysis on Diploid Biallelic SNP data.
... It is Poppr package in R. I am trying the stratification of populations and sub populations for running AMOVA test using. I have my file named mosrap21 so running the command > strata(monsrap21) <- data.frame(other(monsrap21)$population_hierarchy) It is giving the Error: Number of rows in da ...
written 14 months ago by umermehar100
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R for Amova Analysis on Diploid Biallelic SNP data.
... I am using Popper program. Unable to Complete data stratification. As I am using data from plant origin without clonal attributes. kindly help in this regard ...
R amova snp written 14 months ago by umermehar100

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